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diff --git a/src/analysis/cf_nvo.c b/src/analysis/cf_nvo.c
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+/*******************************************************************************
+ * Johns Hopkins University
+ * Center For Astrophysical Sciences
+ * FUSE
+ *******************************************************************************
+ *
+ * Usage: cf_nvo all_segments.fit nvo_file.fit
+ *
+ * Description: Write a National Virtual Observatory (nvo) file. The program
+ * uses the file created by cf_pack, which contains one spectrum
+ * per extension, each corresponding to a detector channel.
+ *
+ * History: 04/11/05 tc v1.0 First release
+ * 05/16/2005 wvd v1.1 Check mean flux of each segment.
+ * If preferred channel is missing,
+ * replace it with another.
+ * 05/19/2005 wvd v1.2 Shift each channel to match
+ * LiF1A between 1045 and 1070 A.
+ * 05/20/2005 wvd v1.3 For emission-line sources,
+ * cross-correlate on O VI lines.
+ * 05/23/2005 wvd v1.4 Don't assume that sides A and B
+ * have the same shift.
+ * 06/01/2005 wvd v1.5 Do assume that sides A and B
+ * have the same shift.
+ * 06/03/2005 wvd v1.6 Delete unused variables.
+ * 06/08/2005 wvd v1.7 Define MAXFLOAT if needed.
+ * 06/16/2005 wvd v1.8 Include values.h
+ * 07/06/2005 wvd v1.9 If FESCENT = FES B, use LiF 2B
+ * as wavelength standard.
+ * 07/12/2005 wvd v1.10 Give up on use of MAXFLOAT.
+ * 08/11/2005 wvd v1.11 Set keyword NEXTEND = 1.
+ * 03/22/2006 wvd v1.12 Allow use of SiC data for
+ * 1000-1100 A region.
+ * Don't cross-correlate segments
+ * with OBSTIME = 0.
+ * 05/16/2006 wvd v1.13 Use Lyman beta to align
+ * background exposures.
+ * Use O VI and C II to align WD's.
+ * 05/19/2006 wvd v1.14 In copy_spec(), test index to
+ * prevent extending past the edge.
+ * For BKGD targets, omit flux
+ * comparison when deciding which
+ * regions to use.
+ * Delete index to the file
+ * extensions from the primary HDU.
+ * Compute mean flux over same
+ * wavelength region for each band.
+ * 05/24/2006 wvd v1.16 For PC targets, don't include
+ * O VI in calculation of mean flux
+ * 12/19/2006 wvd v1.17 Reject segments with
+ * OBSTIME < 10 seconds when full
+ * exposure is longer than 100 s.
+ * 02/19/2008 bot v1.18 Fixed indexing problem in
+ * copy_spec due to shift and n_copy
+ *
+ ******************************************************************************/
+
+#include <math.h>
+#include <string.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include "calfuse.h"
+
+#define MAXSHIFT 30
+#define N_SHIFT 61
+#define NVO_MIN 900
+#define NVO_MAX 1190
+
+static char CF_PRGM_ID[] = "cf_nvo";
+static char CF_VER_NUM[] = "1.18";
+
+static int
+compute_shift(fitsfile *pt_fits, int hdu_ref, int hdu, float wmin, float wdelta,
+ float wpc, int *shift, int *quality)
+{
+ char comb[FLEN_VALUE], ref_comb[FLEN_VALUE];
+ int hdutype, status = 0;
+ int ind_chi2_min, nchi;
+ long i, k, n_rows, ref_start, start, n_pix;
+ float *error, *flux, *wave, *ref_error, *ref_flux, *ref_wave;
+ float chi_square[N_SHIFT], chi_square_min, chi_square_max;
+ float ref_obstime, obstime;
+ double scale, sum, var1, var2;
+
+ /* Don't need to shift reference spectrum. */
+ if (hdu_ref == hdu) {
+ *shift = 0;
+ *quality = TRUE;
+ return(0);
+ }
+
+ /* Read data for reference and data channels. */
+ FITS_movabs_hdu(pt_fits, hdu_ref, &hdutype, &status);
+ FITS_read_key(pt_fits, TSTRING, "COMBMETH", &ref_comb, NULL, &status);
+ FITS_read_key(pt_fits, TFLOAT, "OBSTIME", &ref_obstime, NULL, &status);
+ n_rows = cf_read_col(pt_fits, TFLOAT, "WAVE", (void **) &ref_wave);
+ n_rows = cf_read_col(pt_fits, TFLOAT, "FLUX", (void **) &ref_flux);
+ n_rows = cf_read_col(pt_fits, TFLOAT, "ERROR", (void **) &ref_error);
+
+ FITS_movabs_hdu(pt_fits, hdu, &hdutype, &status);
+ FITS_read_key(pt_fits, TSTRING, "COMBMETH", &comb, NULL, &status);
+ FITS_read_key(pt_fits, TFLOAT, "OBSTIME", &obstime, NULL, &status);
+ n_rows = cf_read_col(pt_fits, TFLOAT, "WAVE", (void **) &wave);
+ n_rows = cf_read_col(pt_fits, TFLOAT, "FLUX", (void **) &flux);
+ n_rows = cf_read_col(pt_fits, TFLOAT, "ERROR", (void **) &error);
+
+ /* If either channel was not constructed using cross-correlation,
+ * return a shift of 0. */
+ if (strncmp(ref_comb,"X",1) || strncmp(comb,"X",1)) {
+ *shift = 0;
+ *quality = FALSE;
+ printf("hdu = %d, hdu_ref = %d, COMBMETH != XCORR\n",
+ hdu, hdu_ref);
+ return(0);
+ }
+
+ /* If either channel has OBSTIME = 0, return a shift of 0. */
+ if (ref_obstime < 1 || obstime < 1) {
+ *shift = 0;
+ *quality = FALSE;
+ if (ref_obstime < 1)
+ printf("hdu_ref = %d, OBSTIME = %f\n", hdu_ref, ref_obstime);
+ if (obstime < 1) printf("hdu = %d, OBSTIME = %f\n", hdu, obstime);
+ return(0);
+ }
+
+ /* Compute chi-squared for shifts between +/- MAXSHIFT pixels. */
+ ref_start = cf_nlong((wmin - ref_wave[0]) / wpc) + MAXSHIFT;
+ start = cf_nlong((wmin - wave[0]) / wpc);
+ n_pix = cf_nlong(wdelta / wpc) - (N_SHIFT - 1);
+
+ for (k = 0; k < N_SHIFT; k++) {
+ nchi = 0;
+ sum = 0;
+ for (i = 0; i < n_pix; i++) {
+ var1 = ref_error[ref_start + i] * ref_error[ref_start + i];
+ var2 = error[start + i + k] * error[start + i + k];
+ if ((var1 + var2) > 0.) {
+ sum += (ref_flux[ref_start + i] - flux[start + i + k]) *
+ (ref_flux[ref_start + i] - flux[start + i + k]) /
+ (var1 + var2);
+ nchi++;
+ }
+ }
+ scale = (double) nchi / n_pix;
+ chi_square[k] = sum / scale;
+ }
+
+ /* If chi-squared changes by less than 20% over range of shifts, abort.
+ * Otherwise, return shift corresponding to lowest value of chi-square.
+ */
+ ind_chi2_min = 0;
+ chi_square_min = 1E5;
+ chi_square_max = -1E5;
+ for (k = 0; k < N_SHIFT; k++) {
+ if (chi_square[k] < chi_square_min)
+ {
+ chi_square_min = chi_square[k];
+ ind_chi2_min = k;
+ }
+ else if (chi_square[k] > chi_square_max)
+ chi_square_max = chi_square[k];
+ }
+
+ if (chi_square_max / chi_square_min < 1.2) {
+ *shift = 0;
+ *quality = FALSE;
+ printf("hdu = %d, hdu_ref = %d. Chi-square dist is flat.\n",
+ hdu, hdu_ref);
+ }
+ else {
+ *shift = ind_chi2_min - MAXSHIFT;
+ *quality = TRUE;
+ }
+
+ free(ref_error);
+ free(ref_flux);
+ free(ref_wave);
+ free(error);
+ free(flux);
+ free(wave);
+
+ return(0);
+}
+
+
+static int
+copy_spec(fitsfile *pt_fits, int hdu, float w_min, float w_max, float wpc,
+ int shift, float *flux_nvo, float *error_nvo, long n_nvo)
+{
+ int hdutype, status = 0;
+ long i, i0, n_rows, nvo_start, start, n_copy, n_copy0;
+ float *error, *flux, w0;
+
+ FITS_movabs_hdu(pt_fits, hdu, &hdutype, &status);
+ FITS_read_key(pt_fits, TFLOAT, "W0", &w0, NULL, &status);
+ n_rows = cf_read_col(pt_fits, TFLOAT, "FLUX", (void **) &flux);
+ n_rows = cf_read_col(pt_fits, TFLOAT, "ERROR", (void **) &error);
+
+ nvo_start = cf_nlong(((double) w_min - NVO_MIN) / wpc);
+ start = cf_nlong(((double) w_min - w0) / wpc);
+ n_copy = cf_nlong(((double) w_max - w_min) / wpc) + 1;
+ if (nvo_start + n_copy > n_nvo) {
+ printf ("HDU = %d, w_min = %.1f, w_max = %.1f, wpc = %5.3f\n",
+ hdu, w_min, w_max, wpc);
+ printf ("n_nvo = %ld, nvo_start = %ld, start = %ld, n_copy = %ld\n",
+ n_nvo, nvo_start, start, n_copy);
+ cf_if_error("Can't create NVO array.");
+ }
+
+ n_copy0 = n_copy;
+ if (start + shift + n_copy > n_rows) {
+ n_copy = n_rows - (start + shift);
+ if (hdu == 3) for (i = n_copy; i < n_copy0; i++) {
+ flux_nvo[i+nvo_start] = 0.0;
+ error_nvo[i+nvo_start] = 0.0;
+ }
+ }
+
+ i0 = 0;
+ if (start + shift < 0) {
+ i0 = -(start + shift);
+ for (i = 0; i < i0; i++) {
+ flux_nvo[i+nvo_start] = 0.0;
+ error_nvo[i+nvo_start] = 0.0;
+ }
+ }
+
+ for (i = i0; i < n_copy; i++) {
+ flux_nvo[i+nvo_start] = flux[i+start+shift];
+ error_nvo[i+nvo_start] = error[i+start+shift];
+ }
+
+ free(error);
+ free(flux);
+ return(0);
+}
+
+
+int main(int argc, char *argv[])
+{
+ /* Variables */
+ char program[FLEN_VALUE];
+ double mean_flux[8], sum_flux;
+ float *wave, *flux, w0, wpc, hdu_wpc;
+ float *wave_nvo, *flux_nvo, *error_nvo;
+ float max_obstime, wmin, wdelta;
+ long n_rows, n_nvo;
+ int ref, i, nextend=1, n_hdus, shift[8], quality[8];
+ int bkgd_obs=FALSE, objclass;
+ int nkeys, morekeys=0;
+ long k, n_elem;
+
+ char *ttype[] = { "WAVE", "FLUX", "ERROR" };
+ char *tform[] = { "1E", "1E", "1E" };
+ char *tunit[] = { "ANGSTROMS", "ERG/CM2/S/A", "ERG/CM2/S/A" };
+
+ /* HDU numbers must be consistent with output of cf_pack. */
+ char *extname[] = { "1ASIC", "2BSIC", "1ALIF", "2BLIF", "1BSIC", "2ASIC", "1BLIF", "2ALIF" };
+ int hdu[] = { 6, 8, 2, 4, 7, 9, 3 , 5 };
+ float w_min[] = { 997, 1010, 990, 990, 904, 917.5, 1094 , 1090 };
+ float w_max[] = { 1090, 1104, 1080, 1074, 992, 998, 1190 , 1180 };
+
+ /* Regions to use when computing mean flux. */
+ float *region;
+ float region_array[8][6] = {
+ {0, 0, 1030, 1039, 1045, 1070}, /* 1ASIC */
+ {0, 0, 1030, 1039, 1045, 1070}, /* 2BSIC */
+ {0, 0, 1030, 1039, 1045, 1070}, /* 1ALIF */
+ {0, 0, 1030, 1039, 1045, 1070}, /* 2BLIF */
+ {912, 935, 955, 970, 980, 985}, /* 1BSIC */
+ {912, 935, 955, 970, 980, 985}, /* 2ASIC */
+ {1095, 1130, 1140, 1165, 1170, 1180}, /* 1BLIF */
+ {1095, 1130, 1140, 1165, 1170, 1180} /* 2ALIF */
+ };
+
+ char in_name[80], out_name[80];
+ char extname_key[80], src_type[FLEN_VALUE], sp_type[FLEN_VALUE], fescent[FLEN_VALUE];
+ fitsfile *pt_fits, *pt_fits_out;
+ int status = 0, hdutype;
+
+
+ /***********************************
+ ** Enter a timestamp into the log **
+ ***********************************/
+ cf_timestamp(CF_PRGM_ID, CF_VER_NUM, "Begin Processing");
+ cf_error_init(CF_PRGM_ID, CF_VER_NUM, stderr);
+
+
+ /***********************************************************
+ ** Check for proper command-line usage and read arguments **
+ ***********************************************************/
+ if (argc != 3)
+ cf_if_error("Usage: cf_nvo all_segments.fit nvo_file.fit");
+
+ strcpy(in_name, argv[1]);
+ strcpy(out_name, "!");
+ strcat(out_name, argv[2]); /* Force overwrite */
+
+ /*******************************************
+ ** Open input file, read header keywords. **
+ *******************************************/
+ FITS_open_file(&pt_fits, in_name, READONLY, &status);
+ FITS_read_key(pt_fits, TSTRING, "PRGRM_ID", &program, NULL, &status);
+ FITS_read_key(pt_fits, TINT, "OBJCLASS", &objclass, NULL, &status);
+ FITS_read_key(pt_fits, TSTRING, "SP_TYPE", &sp_type, NULL, &status);
+ FITS_read_key(pt_fits, TSTRING, "SRC_TYPE", &src_type, NULL, &status);
+ FITS_read_key(pt_fits, TFLOAT, "OBSTIME", &max_obstime, NULL, &status);
+ FITS_read_key(pt_fits, TFLOAT, "WPC", &wpc, NULL, &status);
+ FITS_read_key(pt_fits, TSTRING, "FESCENT", &fescent, NULL, &status);
+ ref = 2; /* LiF 1A */
+ if (!strncmp(fescent, "FES B", 5)) ref = 3; /* LiF 2B */
+
+ /****************************************************************
+ ** If SRC_TYPE = PC, exclude O VI in calculation of mean flux. **
+ ****************************************************************/
+ if (!strncmp(src_type, "PC", 2))
+ for (i = 0; i < 4; i++)
+ region_array[i][2] = region_array[i][3] = 0;
+
+ /***************************************
+ ** Compute mean flux in each channel. **
+ ***************************************/
+ FITS_get_num_hdus(pt_fits, &n_hdus, &status);
+ if (n_hdus != 9)
+ cf_if_error("Input file must have 9 extensions (%d found)", n_hdus);
+
+ for (i = 0; i < 8; i++) {
+ float obstime;
+ FITS_movabs_hdu(pt_fits, hdu[i], &hdutype, &status);
+ FITS_read_key(pt_fits, TSTRING, "EXTNAME", extname_key, NULL, &status);
+ if (strcmp(extname_key, extname[i]))
+ cf_if_error("Extension %d's name does not match (%s)",
+ hdu[i], extname[i]);
+ FITS_read_key(pt_fits, TFLOAT, "WPC", &hdu_wpc, NULL, &status);
+ if (hdu_wpc != wpc)
+ cf_if_error("Extension %d's WPC does not match primary HDU",
+ hdu[i]);
+ FITS_read_key(pt_fits, TFLOAT, "OBSTIME", &obstime, NULL, &status);
+ if (obstime < 1. || (obstime < 10 && max_obstime > 100))
+ mean_flux[i] = -1;
+ else {
+ n_rows = cf_read_col(pt_fits, TFLOAT, "WAVE", (void **) &wave);
+ n_rows = cf_read_col(pt_fits, TFLOAT, "FLUX", (void **) &flux);
+
+ sum_flux = n_elem = 0;
+ region = region_array[i];
+ for (k = 0; k < n_rows; k++)
+ {
+ if ((wave[k] > region[0] && wave[k] < region[1]) ||
+ (wave[k] > region[2] && wave[k] < region[3]) ||
+ (wave[k] > region[4] && wave[k] < region[5])) {
+ sum_flux += flux[k];
+ n_elem ++;
+ }
+ }
+
+ mean_flux[i] = sum_flux / n_elem;
+ free(wave);
+ free(flux);
+ }
+
+ printf("%s\tmean_flux = %g\n", extname_key, mean_flux[i]);
+ }
+
+ /*******************************************************************
+ * If FESCENT = FES A, compute shifts relative to LiF 1A.
+ * If FESCENT = FES B, use LiF 2B.
+ * For background targets, compare Lyman beta lines.
+ * For other emission-line targets, compare O VI lines.
+ * For white dwarfs, use O VI and C II.
+ * For other continuum sources, use the region between 1045 and 1070 A
+ * for the four 1000-1100 A channels.
+ ******************************************************************/
+
+ if (src_type[1] == 'E') { /* Emission-line source */
+ /* Use Lyman beta to align background observations. */
+ if (objclass == 7 || (program[0] == 'S' && program[2] == '0' && program[3] == '5')) {
+ printf("Assuming background observation.\n");
+ wmin = 1024.;
+ wdelta = 6.;
+ } else { /* Use O VI emission for everything else. */
+ printf("SRC_TYPE = %s. Emission-line target.\n", src_type);
+ wmin = 1030.;
+ wdelta = 9.;
+ }
+ }
+ /* Continuum source */
+ else if (objclass == 17 || objclass == 29 || objclass == 37) {
+ /* Use O VI and C II to align white dwarf spectra. */
+ printf("OBJCLASS = %d. Assuming nearby white dwarf.\n", objclass);
+ wmin = 1030.;
+ wdelta = 9.;
+ }
+ else { /* Use 1045-1070 A region for all other continuum sources. */
+ printf("SRC_TYPE = %s. Continuum target.\n", src_type);
+ wmin = 1045.;
+ wdelta = 25.;
+ }
+
+ for (i = 0; i < 4; i++) {
+ if (mean_flux[i] > -1)
+ compute_shift(pt_fits, hdu[ref], hdu[i], wmin, wdelta, wpc, shift+i, quality+i);
+ else
+ shift[i] = 0;
+ shift[i+4] = shift[i];
+ printf("hdu = %d, hdu_ref = %d, shift = %d\n", hdu[i], hdu[ref], shift[i]);
+ }
+
+ /**************************
+ ** Set up output arrays. **
+ **************************/
+ n_nvo = cf_nlong((double) (NVO_MAX - NVO_MIN) / wpc) + 1;
+ wave_nvo = (float *) cf_calloc(n_nvo, sizeof(float));
+ for (i = 0; i < n_nvo; i++) wave_nvo[i] = NVO_MIN + (double) wpc * i;
+ flux_nvo = (float *) cf_calloc(n_nvo, sizeof(float));
+ error_nvo = (float *) cf_calloc(n_nvo, sizeof(float));
+
+ for (i = 0; i < n_nvo; i++) {
+ flux_nvo[i] = 0.0;
+ error_nvo[i] = 0.0;
+ }
+
+ /**************************************************************
+ ** In each wave band, copy best data set into output arrays. **
+ **************************************************************/
+ /* For BKGD targets, omit flux comparison when selecting which
+ regions to use. */
+ if (objclass == 7 || !strncmp(sp_type, "BKGD", 4)) bkgd_obs = TRUE;
+
+ /* First fill in the 1010-1104 A region with SiC 2B. */
+ copy_spec(pt_fits, hdu[1], w_min[1], w_max[1], wpc, shift[1], flux_nvo, error_nvo, n_nvo);
+
+ /* Replace with SiC 1A if possible. It has a higher S/N, but extends only to 1090 A. */
+ if ((bkgd_obs && mean_flux[0] > -1) || (mean_flux[0] > 0.9 * mean_flux[1]))
+ copy_spec(pt_fits, hdu[0], w_min[0], w_max[0], wpc, shift[0], flux_nvo, error_nvo, n_nvo);
+
+ /* Next overlay the region between 990 and 1080 A with LiF 1A or LiF 2B, if available. */
+ if ((bkgd_obs && mean_flux[2] > -1) || ((mean_flux[2] > 0.9 * mean_flux[3]) &&
+ (mean_flux[2] > 0.7 * mean_flux[0]) && (mean_flux[2] > 0.7 * mean_flux[1])))
+ copy_spec(pt_fits, hdu[2], w_min[2], w_max[2], wpc, shift[2], flux_nvo, error_nvo, n_nvo);
+ else if ((bkgd_obs && mean_flux[3] > -1) ||
+ ((mean_flux[3] > 0.7 * mean_flux[0]) && (mean_flux[3] > 0.7 * mean_flux[1])))
+ copy_spec(pt_fits, hdu[3], w_min[3], w_max[3], wpc, shift[3], flux_nvo, error_nvo, n_nvo);
+ else
+ w_max[5] = 1010, w_min[6] = w_min[7] = 1104;
+ /* If no LiF data, adopt limits of SiC spectra. */
+
+ /* Use SiC 1B to populate the shortest wavelengths. */
+ copy_spec(pt_fits, hdu[4], w_min[4], w_max[4], wpc, shift[4], flux_nvo, error_nvo, n_nvo);
+
+ /* If SiC 2A is good, use it for the main part of 900 - 1000 A. */
+ if ((bkgd_obs && mean_flux[5] > -1) || (mean_flux[5] > 0.9 * mean_flux[4]))
+ copy_spec(pt_fits, hdu[5], w_min[5], w_max[5], wpc, shift[5], flux_nvo, error_nvo, n_nvo);
+
+ /* Use LiF 1B to populate the longest wavelengths. */
+ copy_spec(pt_fits, hdu[6], w_min[6], w_max[6], wpc, shift[6], flux_nvo, error_nvo, n_nvo);
+
+ /* If LiF 2A is good, use it for the main part of 1100 - 1180 A. */
+ if ((bkgd_obs && mean_flux[7] > -1) || (mean_flux[7] > 0.9 * mean_flux[6]))
+ copy_spec(pt_fits, hdu[7], w_min[7], w_max[7], wpc, shift[7], flux_nvo, error_nvo, n_nvo);
+
+
+ for (i = 0; i < n_nvo; i++) {
+ if (flux_nvo[i] >= 1 || error_nvo[i] >= 1) cf_if_error("Bad values in NVO array.");
+ }
+
+ /*********************
+ ** Create NVO file. **
+ *********************/
+ FITS_create_file(&pt_fits_out, out_name, &status);
+ FITS_movabs_hdu(pt_fits, 1, &hdutype, &status);
+ FITS_copy_header(pt_fits, pt_fits_out, &status);
+ FITS_update_key(pt_fits_out, TINT, "NEXTEND", &nextend, NULL, &status);
+ FITS_update_key(pt_fits_out, TSTRING, "FILENAME", (out_name + 1), NULL, &status);
+ FITS_update_key(pt_fits_out, TSTRING, "FILETYPE", "NVO SPECTRUM", NULL, &status);
+ w0 = NVO_MIN;
+ FITS_update_key(pt_fits_out, TFLOAT, "W0", &w0, NULL, &status);
+
+ /* Delete index to file extensions from the primary HDU. */
+ fits_get_hdrspace(pt_fits_out, &nkeys, &morekeys, &status);
+ for (i = nkeys; i > nkeys-12; i--) fits_delete_record(pt_fits_out, i, &status);
+
+ FITS_create_tbl(pt_fits_out, BINARY_TBL, n_nvo, 3, ttype, tform, tunit, "FUSE_SPECTRUM", &status);
+ FITS_write_col(pt_fits_out, TFLOAT, 1, 1L, 1L, n_nvo, wave_nvo, &status);
+ FITS_write_col(pt_fits_out, TFLOAT, 2, 1L, 1L, n_nvo, flux_nvo, &status);
+ FITS_write_col(pt_fits_out, TFLOAT, 3, 1L, 1L, n_nvo, error_nvo, &status);
+
+ free(wave_nvo);
+ free(flux_nvo);
+ free(error_nvo);
+
+ FITS_close_file(pt_fits_out, &status);
+ FITS_close_file(pt_fits, &status);
+
+ return(0);
+}
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